From ec373635a4b3e095cfcc87ae03bd52b05389e5d1 Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Mon, 30 Oct 2017 11:09:53 +0000
Subject: bugfixes for AstraDevice use
---
src/Python/ccpi/reconstruction/AstraDevice.py | 36 +++++++++++---------
src/Python/ccpi/reconstruction/DeviceModel.py | 3 +-
.../ccpi/reconstruction/FISTAReconstructor.py | 28 ++++++++--------
src/Python/test/test_reconstructor.py | 39 +++++++++++++++++++---
4 files changed, 71 insertions(+), 35 deletions(-)
(limited to 'src')
diff --git a/src/Python/ccpi/reconstruction/AstraDevice.py b/src/Python/ccpi/reconstruction/AstraDevice.py
index 999533b..ac9206e 100644
--- a/src/Python/ccpi/reconstruction/AstraDevice.py
+++ b/src/Python/ccpi/reconstruction/AstraDevice.py
@@ -1,5 +1,6 @@
import astra
from ccpi.reconstruction.DeviceModel import DeviceModel
+import numpy
class AstraDevice(DeviceModel):
'''Concrete class for Astra Device'''
@@ -17,7 +18,7 @@ class AstraDevice(DeviceModel):
self.proj_geom = astra.creators.create_proj_geom(
device_type,
self.acquisition_data_geometry['detectorSpacingX'],
- self.acquisition_data_geometry['detectorSpacingX'],
+ self.acquisition_data_geometry['detectorSpacingY'],
self.acquisition_data_geometry['cameraX'],
self.acquisition_data_geometry['cameraY'],
self.acquisition_data_geometry['angles'],
@@ -34,10 +35,15 @@ class AstraDevice(DeviceModel):
Uses Astra-toolbox
'''
- sino_id, y = astra.creators.create_sino3d_gpu(
- volume, self.proj_geom, self.vol_geom)
- astra.matlab.data3d('delete', sino_id)
- return y
+
+ try:
+ sino_id, y = astra.creators.create_sino3d_gpu(
+ volume, self.proj_geom, self.vol_geom)
+ astra.matlab.data3d('delete', sino_id)
+ return y
+ except Exception(e):
+ print(e)
+ print("Value Error: ", self.proj_geom, self.vol_geom)
def doBackwardProject(self, projections):
'''Backward projects the projections according to the device geometry
@@ -49,27 +55,25 @@ Uses Astra-toolbox
projections,
self.proj_geom,
self.vol_geom)
+
astra.matlab.data3d('delete', idx)
return volume
def createReducedDevice(self):
- proj_geom = astra.creators.create_proj_geom(
- device_type,
- self.acquisition_data_geometry['detectorSpacingX'],
- self.acquisition_data_geometry['detectorSpacingX'],
+ proj_geom = [
self.acquisition_data_geometry['cameraX'],
1,
- self.acquisition_data_geometry['angles'],
- )
+ self.acquisition_data_geometry['detectorSpacingX'],
+ self.acquisition_data_geometry['detectorSpacingY'],
+ self.acquisition_data_geometry['angles']
+ ]
- vol_geom = astra.creators.create_vol_geom(
+ vol_geom = [
self.reconstructed_volume_geometry['X'],
self.reconstructed_volume_geometry['Y'],
1
- )
- return AstraDevice(proj_geom['type'] ,
- proj_geom,
- vol_geom)
+ ]
+ return AstraDevice(self.type, proj_geom, vol_geom)
diff --git a/src/Python/ccpi/reconstruction/DeviceModel.py b/src/Python/ccpi/reconstruction/DeviceModel.py
index 6214437..eeb9a34 100644
--- a/src/Python/ccpi/reconstruction/DeviceModel.py
+++ b/src/Python/ccpi/reconstruction/DeviceModel.py
@@ -28,7 +28,8 @@ HELICAL'''
Mandatory parameters are:
device_type from DeviceType Enum
-data_acquisition_geometry: tuple (camera_X, camera_Y)
+data_acquisition_geometry: tuple (camera_X, camera_Y, detectorSpacingX,
+ detectorSpacingY, angles)
reconstructed_volume_geometry: tuple (dimX,dimY,dimZ)
'''
self.device_geometry = device_type
diff --git a/src/Python/ccpi/reconstruction/FISTAReconstructor.py b/src/Python/ccpi/reconstruction/FISTAReconstructor.py
index d2eefc0..0607003 100644
--- a/src/Python/ccpi/reconstruction/FISTAReconstructor.py
+++ b/src/Python/ccpi/reconstruction/FISTAReconstructor.py
@@ -27,7 +27,7 @@ import numpy
from enum import Enum
import astra
-#from ccpi.reconstruction.AstraDevice import AstraDevice
+from ccpi.reconstruction.AstraDevice import AstraDevice
@@ -90,11 +90,7 @@ class FISTAReconstructor():
self.pars['number_of_angles'] = nangles
self.pars['SlicesZ'] = sliceZ
self.pars['output_volume'] = None
- self.pars['device'] = device
-
-
- reduced_device = device.createReducedDevice()
- self.setParameter(reduced_device_model=reduced_device)
+ self.pars['device_model'] = device
self.use_device = True
@@ -183,6 +179,9 @@ class FISTAReconstructor():
if not 'initialize' in kwargs.keys():
self.pars['initialize'] = False
+ reduced_device = device.createReducedDevice()
+ self.setParameter(reduced_device_model=reduced_device)
+
def setParameter(self, **kwargs):
@@ -455,22 +454,24 @@ class FISTAReconstructor():
'ring_lambda_R_L1'])
t = 1
-
+
device = self.getParameter('device_model')
reduced_device = self.getParameter('reduced_device_model')
for i in range(self.getParameter('number_of_iterations')):
+ print("iteration", i)
X_old = X.copy()
t_old = t
r_old = self.r.copy()
- if self.getParameter('projector_geometry')['type'] == 'parallel' or \
- self.getParameter('projector_geometry')['type'] == 'fanflat' or \
- self.getParameter('projector_geometry')['type'] == 'fanflat_vec':
+ pg = self.getParameter('projector_geometry')['type']
+ if pg == 'parallel' or \
+ pg == 'fanflat' or \
+ pg == 'fanflat_vec':
# if the geometry is parallel use slice-by-slice
# projection-backprojection routine
#sino_updt = zeros(size(sino),'single');
- if self.use_device:
+ if self.use_device :
self.sino_updt = numpy.zeros(numpy.shape(sino), dtype=numpy.float)
for kkk in range(SlicesZ):
@@ -491,6 +492,7 @@ class FISTAReconstructor():
# for divergent 3D geometry (watch the GPU memory overflow in
# ASTRA versions < 1.8)
#[sino_id, sino_updt] = astra_create_sino3d_cuda(X_t, proj_geom, vol_geom);
+
if self.use_device:
self.sino_updt = device.doForwardProject(X_t)
else:
@@ -563,7 +565,7 @@ class FISTAReconstructor():
#sino_updt = zeros(size(sino),'single');
x_temp = numpy.zeros(numpy.shape(X),dtype=numpy.float32)
- if use_device:
+ if self.use_device:
proj_geomT = proj_geom.copy()
proj_geomT['DetectorRowCount'] = 1
vol_geomT = vol_geom.copy()
@@ -581,7 +583,7 @@ class FISTAReconstructor():
x_temp[kkk] = \
reduced_device.doBackwardProject(residual[kkk:kkk+1])
else:
- if use_device:
+ if self.use_device:
x_id, x_temp = \
astra.creators.create_backprojection3d_gpu(
residual, proj_geom, vol_geom)
diff --git a/src/Python/test/test_reconstructor.py b/src/Python/test/test_reconstructor.py
index 343b9bb..f4627d7 100644
--- a/src/Python/test/test_reconstructor.py
+++ b/src/Python/test/test_reconstructor.py
@@ -30,10 +30,10 @@ def createAstraDevice(projector_geometry, output_geometry):
'''TODO remove'''
device = AstraDevice(DeviceModel.DeviceType.PARALLEL3D.value,
- [projector_geometry['DetectorSpacingX'] ,
- projector_geometry['DetectorSpacingY'] ,
+ [projector_geometry['DetectorRowCount'] ,
projector_geometry['DetectorColCount'] ,
- projector_geometry['DetectorRowCount'] ,
+ projector_geometry['DetectorSpacingX'] ,
+ projector_geometry['DetectorSpacingY'] ,
projector_geometry['ProjectionAngles']
],
[
@@ -332,5 +332,34 @@ else:
fistaRecon.prepareForIteration()
- X = fistaRecon.iterate(numpy.load("X.npy"))
- numpy.save("X_out.npy", X)
+ X = numpy.load("X.npy")
+## rd = astradevice.createReducedDevice()
+## print ("rd proj_geom" , rd.proj_geom)
+##
+##
+## rd.doForwardProject(X[0:1])
+## proj_geomT = proj_geom.copy()
+## for ekey in rd.proj_geom.keys():
+## if ekey == 'ProjectionAngles':
+## valrd = numpy.shape(rd.proj_geom[ekey])
+## valg = numpy.shape(proj_geomT[ekey])
+## else:
+## valrd = rd.proj_geom[ekey]
+## valg = proj_geomT[ekey]
+##
+## print ("key {0}: RD {1} geomT {2}".format(ekey, valrd, valg))
+##
+##
+## proj_geomT['DetectorRowCount'] = 1
+## vol_geomT = vol_geom.copy()
+## vol_geomT['GridSliceCount'] = 1;
+## rd.proj_geom = proj_geomT.copy()
+## rd.vol_geom = vol_geomT.copy()
+##
+##
+##
+## sino_id, y = astra.creators.create_sino3d_gpu(
+## X[0:1], rd.proj_geom, rd.vol_geom)
+
+ X = fistaRecon.iterate(X)
+ #numpy.save("X_out.npy", X)
--
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